Kitsune Empress
by Zero Arashi Uchiha
Summary: kidnapped and experimented on, a child will become a apex predator like no other. The creature will become a woman in the eyes of the world however she would forever be a monster but something greater and terrifying, Naruko Uzumaki will show the world the might and strength of a new empress
1. Chapter 1

**An: Based on "Fox Queen" written by flashfox tyrell05 I wanted to write it I couldn't get this story out of my head given how Fox Queen intrigued me so much that it made me want to do another Naruto X Alien Crossover so I'm giving this story a shot I promise you, you will enjoy my version of "Fox Queen" with a reference of "Abomination" but instead I dubbed it as "Kitsune Empress" I hope you enjoy it cause there will be powerful strong Naruko and I'm also adding a little Species or star craft to the story like give Naruko Sarah kerrigan's powers and element like bloodlines I will explain more when I reach a certain part of the story or chapter**

 **parings undecided or I could make it a flat out harem.**

 **Story Title: Kitsune Empress**

 **Summary: kidnapped and experimented on, a child will become a apex predator like no other. The creature will become a woman in the eyes of the world however she would forever be a monster but something greater and terrifying, Naruko Uzumaki will show the world the might and strength of a new empress.**

 **Rated: M.**

 **Parings undecided might make it a harem.**

 **Prologue.**

" Oh my kami..." Sarutobi Hiruzen whispered with horror, disgusted in what his old rival had done Beyond what he had been prior. Having finally found a piece of hard evidence against Danzo, The sandaime had led an aggressive and offensive investigation against the old war hawk eventually getting enough evidence to lead a raid on the man's Root facilities. Among them was a laboratory hidden deep within the hokage monument. After infiltrating the place with several dozen Anbu that were only loyal to the Hokage himself and handful of jonins the hokage had hand-picked for the operation, they struck, arresting those they could and killing those they couldn't. Several of them had committed suicide, biting down a poison tooth to end their lives before they could be questioned.

But that wasn't what sickened "The Professor"

It was the occupant of the liquid-filled glass obelisk set before him.

Appearing to be between the ages of 6 or 7 was a child with three whisker marks on each cheek, black hair, blonde kitsune ears with black tips on the child's head, eyes were colored obsidian cat like with black slit puplis, nails were pointed and sharp colored black, skin was pale and what else did the child had?. A six foot tail that was black with a blade at the end of it, five digit hands too.

Hiruzen couldn't believe what his old eyes were seeing this child looked like his surrogate grandson Naruto Uzumaki except.. this Naruto he was looking at now in the container was a female.

" Is that... No... It can't be..." Itachi Uchiha muttered in shock behind his anbu weasel mask looking at Naruto as he approached removing his mask from his face to see the person with both eyes.

" Naruto..." Hiruzen whispered, still shocked and couldn't believe what his old rival had done to the child he once considered a surrogate grandson.

"Hokage-sama, we must let her out!" Exclaimed Yugao who was code named Neko while Hiruzen glanced at the red button that said 'release' across it in bright yellow lettering and flipping the clear Plexi glass cover and and pressed the large button with his hand as the liquid in the container was draining with itachi now opening the container to pulling Naruto out who was still sleep as if she was in a coma. The uchiha cradled naruto in his arms looking at his comrades and Hokage until Kakashi and his squad of anbu appeared.

" Hokage-sama Danzo has escaped we failed..." He said bowing respectfully towards his leader with the anbu doing the same while Hiruzen growled with a scowl on his face that his old rival had escaped.

" Orders sir?" Asked Yugao with hiruzen turning to her.

" Find what else Danzo has been hiding and keeping down here and find anyone else who was a victim in his cruel experiments until you do destroy this laboratory and everything in it!" Spoke Hiruzen with furious anger with his Anbu and Jonins nodding leaving the Hokage with Itachi and Yugao.

" What are we going to do about her Hokage-sama? she seems to be in a coma..." Said Yugao with him now sighing sadly looking at Naruto.

" We will return her to the village and take her to the hospital... I may have to contact Tsunade if our medics fail to wake Naruto out of her coma..." He said grimly

" What of Danzo?" Itachi now spoke

" He will be labeled as a traitor for the crime he has done..." The Hokage replied with venom still furious at his old rival.

" Let's go... It seems I have to start a meeting with the council and inform them this however Yugao and Itachi you two take Naruto to the hospital and guard her when the meeting is over I will come to the hospital." He said with them nodding as Itachi carried Naruto in bridal style walking out the lab with Yugao following him.

( Council chamber)

Sarutobi Hiruzen had summoned both sides of his council, the shinobi council and the civilian council along side of them were the elders the Hokage's advisors Homura and Koharu the only elder missing was Danzo.

" Thank you all for coming on such short notice.. this is an emergency meeting which is why I have summoned you all here." Hiruzen said in a serious tone looking at both councils who tensed under his tone.

" What seems to be the problem Hokage-sama?" Asked a civilian council member while the fire shadow sighed at what he was going to say.

" The reason I have summoned you all is to discuss an S-rank secret and if it leaves this council chamber you will be killed on the spot.. do I make myself perfectly clear?" Said Hiruzen with seriousness in his tone while leaking killer intent to get the message through both councils as they flinched at his tone and they knew if they spoke of the secret they would be killed.

" What's so important about this secret Hokage-sama?" Asked Fugaku Uchiha who raised a eyebrow and was anxious about the secret.

Before Hiruzen could speak Homura interrupted him by saying.

" Where's Danzo? it's not like him to be late?" Spoke the old elder while his friend Koharu wanted to know where was the old warhawk.

" This discussion is very much about Danzo and what he has done." Said Hiruzen with venom in his tone at the mention of his former team mate as both councils turned to him looking tensed.

" What has Danzo done Hokage-sama?" Asked Shikaku who had a feeling the old war hawk had done something horrible and from the way the Hokage said Danzo's name might confirm his suspicion.

" Danzo has committed a treasonous crime and is declared a traitor for what he has done tonight I have discovered that not only he still had Root active but has been keeping orphans in his root facilities molding them into emotionless root anbu. But that's not all he did... he has done what would Orochimaru be proud of... he has experimented on a child." Said Hiruzen with a cold tone earning shocked faces and gasps from everyone in the council room as Hiashi Hyuga now ananswered.

" Who is this child did Danzo experimented on Hokage-sama?" The Hyuga Clan head asked while many in the room wanted to know as well.

" The Child he has been experimenting on was none other than Naruto Uzumaki" He replied with sadness and disgust for what Danzo did.

Both councils looked shocked and horrified.

" Did he tamper with the kyubi's seal?" Asked Inochi Yamanaka

" I do not know... I don't know what he has done but I managed to find this file he documented about Naruto" The old kage said pulling out a file from his robes that had everything about Naruto and on the front of the file was labeled in red handwriting that said. 'Project Empress' laying the file on the table everyone looking in shock.

" Project Empress?" said Shikaku in confusion looking at the file something told him that Danzo may have done something else to Naruto .

" Yes... Naruto is not a male anymore... he is a female now..." muttered Hiruzen making the council gasp

" What the Hell did Danzo do? he turned the pup into a female now?!" Spoke Tsume Inuzuka with shock to make sure she heard that correctly with Hiruzen nodding.

" Where is she now Hokage-sama?" asked Choza while the old kage answered

" She is now being held in the hospital guarded by Weasel and Neko as of right now I will double more anbu to look after her and I myself will check on her... she seems to be in a coma I'm depending on our doctors at the hospital to wake her from her coma and if she doesn't I may have to summon Tsunade Senju back to the village to wake her and summon Jiraiya as well to check the Kyubi's seal to make sure Danzo didn't tamper with it or damage it due to experimenting on her..." He said with many looking a little relieved about what he said.

" This meeting is adjourned and remember this is S-ranked if what was said in this chamber mentioned out in the village you will be put to death understand?" He said getting nods from everyone as he nodded as well.

" Good." He said now getting up from his seat now leaving the council room to go to the hospital.

( Elsewhere out on the borders of Fire country far from konoha)

In a hidden Base where a old man was with a cane, a bandaged face that covered his right eye and his arm in a sling. besides the old man were a group of anbu that had blank masks and the Kanji for Root on their masks as the old man spoke.

" Sai." he said while a pale boy stepped forward to the old man and got on one knee in a bowing position.

" Yes Danzo-sama" Sai replied in a emotionless tone looking up to his master.

" I have a special task for you... and I entrust this mission to you." Danzo stated with a stoic expression.

" What is your bidding Lord Danzo...?" Sai asked.

" You are to return to konoha and be a spy for me I want you to let me know what happens in the village while I am in exile" Danzo said with Sai Nodding

" And I also want you to keep a sharp eye on Project Empress inform me of what she does and her development..." He said with the pale boy nodding.

" As you wish Danzo-sama it will be done" Sai Replied.

" Good now go and do not fail me..." He said in a harsh tone as the boy rose up and went on his way back to Konoha

" What should we do Danzo-sama" Said Fu looking at his master.

" We are going to a new base of operation... strengthen our forces and remain hidden until the time is right to show ourselves..." He said looking up at the clouds

" What of Project Empress?" Spoke Torune

" Do not worry if she were to find out and seek revenge for what I did to her I have a fail-safe incase she lashes out on us I placed a loyalty seal on her so that I could control her she will only listen to me and no else once I have that seal activated." He said with a grin

" Let's go... we must keep going it won't be long till Hiruzen sent hunter nins after me." He said walking now with his army of root behind him.. he hoped his plan will go all he needed to do was wait when the time comes and if his former team mate Hiruzen were to pass away he and his root will reclaim konoha and mold it to his image with Naruto at his side will be a weapon for konoha like he always wanted then rise to the top by making konoha the strongest village and him becoming The new 5th Hokage or 6th Hokage. But first things first he needed to find himself and his root a new base for them to hide in exile.

( Konoha Hospital)

In the Hospital Naruto was in a room still in her coma while the Doctors and Nurse were checking on her like the Hokage ordered though the Anbu were guarding the door while Itachi and Yugao were inside the room watching the doctors as they waited for the Hokage to come and meet them.

He walked in while the doctors, and nurse alongside Itachi and Yugao bowed to him as the first doctor came to him she was a female as he spoke.

" How is she doing Doctor?" he asked.

" She's stable and some what healthy however Hokage-sama there seems to be a problem." She answered to her superior

" What's the problem?" he wondered with a frown

" We can't get her out of her coma we tried everything the only one with the skill of healing and awaking her from her coma would be Tsunade Senju" The doctor said as she held her clipboard writing notes.

" I see... very well I will do my best to contact Tsunade and get her back in the village anything else I need to know doctor?" He said with a sigh.

" We did a few scanning on her Hokage-sama her chakra is very different and her blood is also green and acidic..." She explained while he and the others in the room looked shocked Why is Naruto's blood acidic and green.

"Anything else?" He asked with a look of worry on his face.

" Not so far milord we are still checking on her to see what develops" She replied.

" Very Well... I will take my leave keep me posted on what happens to her" He said with her nodding as he turned to Yugao and Itachi with them bowing.

" You two are in charge consider this a S-rank do not let anyone in this room but me and her doctor understood?" He said with them nodding.

" Good I'm going to my office and make it my business to contact both my former students about this matter" He said walking out the room leaving Itachi and Yugao and the doctors alone with Naruto

Unknown to anyone that Naruto herself twitched and shivered while she was in her coma.

 _To be continued._

 **AN: I hope you all are pleased and enjoyed this story like I said couldn't get it out of my head after reading "Fox Queen" so just so you know in this Story I'm mixing Aliens/ Species/ and maybe a little star craft like give Naruko Sarah kerrigan's powers and Eve's power or personality. since she's already half Xenomorph with Queen status but instead she will be an empress since I made her a combination of Eve, (species), Sarah Kerrigan ( Star craft) and Xenomorph Queen/ Empress (Aliens) . until next time in a few days Elf Kitsune is coming up I haven't forgotten so are you later.**


	2. Chapter 2

**AN: Hello readers** **here is the next chapter I see you guys want me to have the loyalty seal removed from Naruko? *Smirks* well there's a chance I'm not going to remove it... might keep it to pull off a ultimate plot twist or have it removed just for the heck of it as for the pairings or harem it's still some what undecided but maybe later in a certain chapter I'll think about letting it be a harem alright? and don't forget she's a combination of Sil/Eve plus Sarah kerrigan and plus Xenomorph Queen. if you guys don't know who Sil is or Eve watch Species... and Species 2, And the Xenomorph types? Naruko will breed that will be a surprise, *grins* Enjoy the chapter.**

 **Chapter 2: Awakening.**

 **Disclaimer: I don't own Naruto, aliens vs predator, species or star craft.**

Naruto was twisting and turning in her coma while she was in her hospital room alone outside her door were Neko and Weasel on guard like The sandaime stationed them to do. It was midnight everything was quiet and peaceful while Naruto continued to twist and turn in her sleep while she was sweating.

( Flash Back 2 years later)

" _Get out demon! you don't deserve to live here anymore! you can fend for yourself!" Sneered the orphanage owner who closed the door locking it leaving Naruto out on the streets while the blonde boy had little tears coming from his eyes as he walked off to go find himself a place to sleep maybe his Hokage-jii could give him a place to stay in the morning since the orphanage kicked him out he was only 4 years old. Now that he had no place to go he went into the alley way unaware to him that he was being watched by two anbu with blank masks with the kanji for root on them as they jumped from rooftop to rooftop to follow Naruto._

 _Naruto sighed as he sadly looked up at the stars of the night wishing why was he always treated like this he was so confused and sad to why every day he gets treated like this and why does the village hate him so much the only people who never shunned him was the ichiraku ramen restaurant, his Hokage-jiji, Weasel and Neko. Naruto just wished he could be loved, he wanted a family and friends to acknowledge him despite his ambition into becoming Hokage so that everyone can respect him for once and he promised himself that he will make that dream come true._

 _He was about to keep walking until he was suddenly hit in the back of the neck knocking him out cold the last thing he saw before passing out was a anbu with a blank mask._

 _An hour later Naruto found himself strapped to a table looking frightened seeing a bunch of doctors and an old man with a bandaged face, by the old man and doctors were a squad of anbu in blank masks._

 _" Shall we begin the procedure sir?" Asked a Doctor Who was looking at the old man._

 _" Yes begin The procedure Now that we have the kyuubi jinchuriki in our grasp we will see can he survive this experiment since all of our other chosen test subjects died from this procedure so I'm sure the kyuubi jinchuriki won't die from this." Spoke the old man with no emotion in his tone._

 _Naruto looked frightened as he looked up at the doctors now surrounding him with their expressions showing no emotion._

 _" Please don't kill me... I'm a good boy!?" pleaded Naruto making Danzo turn towards him._

 _" Do not worry boy... why would a kill a child with such great potential?" Danzo said with a fake grandfatherly tone._

 _" You're not going to kill me?" Replied Naruto who looked a little relieved until Danzo showed a dark grin._

 _" No, I have other plans for you dear boy I'm going to mold you into the greatest weapon ever." Danzo said while giving a nod to a doctor._

 _The doctor pulled out a syringe filled with a sedative walking towards Naruto._

 _Naruto paled seeing the syringe he tried to get off the table but couldn't due to the restraints on him he struggled trying to break free but before he could try to speak in protest the doctor struck the syringe in Naruto's neck injecting him with the sedative, Once Naruto felt the drug go into him he tried to fight it but couldn't he felt his body not obeying him plus he felt sleepy for some reason and darkness was starting to take him the last thing he saw before his eyes could close was the doctors were closing in on him as he closed his eyes completely._

 _Two Days later._

 _" What's the status?" Asked Danzo who was looking over Naruto's sleeping form._

 _" We are still working on the procedure lord Danzo but there seems to be some complications" Spoke the doctor causing Danzo to frown_

 _" Explain." He said._

 _" Well due to the procedure something is stopping us from completing it" Spoke the doctor_

 _" And that is?" Danzo said not looking pleased with this information._

 _" It's the kyuubi's chakra it's somehow stopping us." He said with Danzo scowling._

 _" Well enforce the infection into him I want to see what develops!" Demanded Danzo_

 _" Lord Danzo with all due respect if we do wouldn't it damage the seal to the kyuubi?" Protested the doctor._

 _" Nonsense... I'm sure nothing will happen to the kyuubi's seal since the yondaime put alot of effort into this seal" Said Danzo now grabbing a large syringe filled with some type of substance into it. As he pulled up Naruto's shirt and without hesitation he sticked the large syringe deep into Naruto's stomach where the seal was injected all of the serum into Naruto every last drop of it._

 _Naruto flinched in his sleep as he felt the syringe impale him and felt his DNA and molecules rearrange once the serum came in contact with his Cells and DNA structure._

 _Danzo pulled out and stared at Naruto with a pleased smile._

 _" Now we will see can you survive this... my future weapon" He said turning to the doctor._

 _" Keep him sedated and let meme know what happens" Danzo said with the doctor nodding as the old war hawk left._

 _A week later._

 _" What's the status how is it coming?" Asked Danzo who now appeared as his one eye widened at what he was seeing._

 _" Her status has increased" The doctor replied while Danzo turned on his sharingan behind his bandaged face_

 _" Her?, what do you mean? He has changed into a female?" Danzo said with rare surprise._

 _" Yes sir the serum you injected him with has rearranged his Dna, Cells and molecules and even changed his gender so therefore he is no longer a Male just a female.." The doctor said going over his report for Danzo._

 _" Anything else?" Danzo asked._

 _" Yes sir her chakra is off the charts sir it's increasing drastically fast and her blood changed Color to green" Spoke the Doctor while Danzo stood there watching Naruto like a hawk absorbing everything the doctor has said._

 _" Anything else?' He asked hoping there was more to this._

 _" None so far my lord..." the doctor replied in a emotionless tone_

 _" I see..." Danzo said sighing a little giving the doctor a glance._

 _" Inform me of what else happens I will be going..." He said with the doctor nodding as he left before giving a dark smile towards Naruto._

 _Two weeks later._

 _Naruto groggily wakes up unaware of his current change he looks around with he vision still blurry. he couldn't remember where was he, he began to speak._

 _" Hello?" He spoke but paused when he realized something why did his voice sound feminine?_

 _" What the hell...?" He spoke again in his female tone with his vision getting better._

 _" So you're awake at last" Spokes voice with her turning towards the one who spoke._

 _it was Danzo._

 _" Who are you and where am I?" he spoke his female tone again._

 _" My name is not important right now my dear weapon.." He said with a smile_

 _" Weapon?" She replied_

 _Yes you are my weapon... and with your great potential you will make all of konoha's enemies tremble in fear" Said Danzo now throwing a mirror to her as she caught it._

 _When she looked at the mirror her eyes widened when she saw her reflection her face looked more feminine. As she looked up at Danzo who was standing there grinning a bit._

 _" What the hell happened to me!? why do I look like a girl!?" Demanded Naruto_

 _" Let's just say I gave you a change to be my perfect weapon and the side effects has changed you to be a young girl" Stated Danzo while she looked horrified._

 _" Is there a way to change me back!?" she shouted with him shaking his head._

 _" No ... you're a woman for the rest of your life" He said with no care in his voice._

 _" N-No this can't be!? there has to be a way!? I don't want to remain a girl!" She said with tears coming out her eyes while Danzo stood there with no expression on his face._

 _" As I said your a woman forever and you will stay that way until the day you die and serve me as my pet" Danzo said smirking_

 _" I don't belong to you!" She shouted in anger._

 _" You are now.. you are root property" Danzo said snapping his fingers with root anbu appearing as they surrounded Naruto while she glanced around seeing she was outnumbered._

 _" Just who the hell are you!? what do you want with me!" She shouted with the root anbu closing in on her with their tanto's out._

 _" I am Danzo Shirima I am your master for you to obey..." He declared. ( An: Sorry if I misspelled his last name)_

 _" No No!" She yelled as the root anbu grabbed her arms ._

 _" Take her away to a new facility" Danzo said with them doing what he said they dragged Naruto as she yelled and screamed at Danzo yelling death threats at him._

 _A month later._

 _Naruto was locked up in a compound with seals all over to prevent her from escaping, numerous times she has tried to escape but couldn't Danzo placed Security seals all over the compound to keep her from breaking free. Her compound is a dark cell designed for her though she has changed she was still pressing to escape out this hell hole and find Hokage-jiji but she doesn't realize she's in konoha since Danzo sealed her away in a new facility so the doctors could run tests on her and study her._

 _" I hate it here..." She said sitting by a wall with claw marks on it._

 _She wished someone could come and rescue her but who? she's been imprisoned here for a month... she's tired of going through tests and be properly conditioned as a weapon like Danzo claimed. She swore if she ever breaks free she will kill him that is if it happens._

 _During her imprisonment here she noticed that she was changing and feeling somewhat different for some odd reason what ever Danzo injected into her was causing another side effect._

 _A year later._

 _Naruto is now 5 years old sitting in the corner of her compound wall with her hair now the color of black, her eyes were now obsidian color with a black silt pupil, her nails looked straight but black and sharp as steel, her skin was no longer tan just pale, on her head she grew fox ears they were blonde with black tips, her hands were 5 digit._

 _But that's not all what changed her she even grew a tail that was longer than her body at the end of her tail was a sharp blade at the end of it as if it was a spear._

 _Nothing else has changed so far until Danzo decided to train her for combat testing against his root anbu to test her strength she was pitted against two of his strongest root anbu Torune and Fu._

 _in her fights she was getting aggressive as if she was an apex predator. Though this isn't the first time she has gone aggressive in combat exercise she was like this towards any root anbu she was paired against she often killed some root anbu in those combat exercises which pleased Danzo seeing this side of her. She has killed 13 root anbu and sent 20 in the root infirmary just by ripping their limbs off or breaking them she vented her pent up anger on root anbu._

 _Given how she was imprisoned inside that compound for a year had changed her , she became merciless, cold, and vicious she even attempted to kill Danzo the moment he released her from the compound for the combat exercise it took him, Torune and Fu to put her down and subdue her._

 _Her eyes held no warmth just no expression in those warm eyes she used to have before she was kidnapped._

 _She didn't even know who she was anymore she wasn't Naruto Uzumaki anymore... the Naruto Uzumaki everyone use to know and love was gone or dead due to her imprisonment and enslavement by Danzo._

 _A day ago she was being sent to a new facility she had chakra cuffs on her she had 30 root anbu escorting her to the new facility her head was covered with a helmet. (AN: think like those helmets from Elfen Lied she's wearing one of those) Now why was she going to another facility? to go through another test and to be experimented on again since Danzo wanted to inject new bloodlines into her to make her stronger since she was checked for a physical by root doctors to be sure she was getting powerful... and healthy to be conditioned as Danzo's weapon._

 _Before she could be locked away in this new facility she thought one thing._

 _" Someday I will break out of here and kill Danzo if it's the last thing I'd do though I won't return to konoha... the villagers will never accept me for what's look like now... maybe I will find a new village or just run off somewhere, where no one can find me... "_

 _Those were her last thoughts before being locked up in a lab and to be experimented once again._

 _( End of Flash back)_

( Hokage Tower)

Hiruzen Sarutobi was writing messages to his two former students to return to konoha he hoped and prayed to kami that he would be able to reason with Tsunade to return to awaken Naruto, though in case Tsunade refuses to return he would have no choice but to mark her in the bingo book and place a bounty on her so high that many missing nins will hunt after her plus send hunter nins after her. He didn't care if she was still grieving over the loss of her lover, brother, kushina and minato, He needed her back now to help Naruto and Jiraiya was needed too so that he could check on the kyuubi seal on Naruto to make sure Danzo didn't tamper with it. And speaking of Danzo... Hiruzen had sent every available hunter nin and Anbu with them to track Danzo down since he is now declared a traitor.

" Danzo... you won't get away with this..!" spat Hiruzen still angry for what Danzo did he kept Naruto locked away in those root facilities. Once Naruto was missing on the night he was kicked out of the orphanage Hiruzen had sent all Anbu and Jonins to find him, he even tried to find Naruto with his crystal ball but couldn't find him still for over two years he has been looking for Naruto everywhere in the village it saddened him to think he lost Naruto and failed Minato and Kushina's dying wish.

But tonight he found Naruto but Naruto is now a female now at first he wanted Inoichi to go into Naruto's memories and see what Danzo did but was thinking that wouldn't be a good idea since the kyuubi could be in Naruto's mind and couldn't risk any chances. Though to say he was worried about Naruto and hoping she would be alright this could have all been avoided had not the orphanage kicked Naruto out and gave Danzo the chance to take Naruto without him knowing.

And the orphanage owner who kicked Naruto out had been arrested and sent to ibiki for torture he assumed that the orphanage owner was probably a accomplice for Danzo.

The old kage sighed as he got done writing his messages to his students and sent his monkey summons to give them their messages as he slumped in his chair looking at the window towards the hospital hoping Naruto would be alright and safe since she is no longer in Danzo's clutches.

An Inuzuka Nin walked in

" Any luck on tracking Danzo?" The sandaime asked with the Inuzuka Nin shaking his head.

" No Hokage-sama we are unable to track him" Spoke the Inuzuka Nin.

" I see... call off the search for now tell everyone to report back to the village" The sandaime said with the dog Nin nodding and walking out .

 _" Where ever you are Danzo I will find you... I will ask Jiraiya for his spy network to find you..."_ Hiruzen said with a thought glancing at a picture of his sensei and team... he wasn't sure if Koharu and Homura were in on this with Danzo he hoped they weren't.

Morning.

( The Hospital)

It was morning with the sun shining through the window while Naruto was still in her bed sleeping and was twitching slightly as her fingers twitched.

 **" I think it's time to wake our Queen up don't you agree?" Said a deep voice in Naruto's mindscape while two three figures were nodding.**

 **" Yes it's time to awaken our successor" Spoke a calm female tone**

 **" I concur with Xeno here... awaken our future empress fox." Said another female voice while the 3rd figure nodded.**

 **" Very well but when will we have a personal talk with my vessel?" Spoke The female voice.**

 **" We will do it the moment she enrolls herself in a academy since the Hokage had found her and saved her from that old man who used our genes to turn her into what she is" Spoke the 3rd figure in a sultry female voice.**

 **" Then it's settled when she graduates from the shinobi academy we will all talk to her understand Xeno and Sil" Said the first figure with purple eyes.**

 **" We understand sarah" Spoke Xeno who was hissing slightly looking at Sarah**

 **" Okay kit it's time for you to wake up." Said the deep female voice.**

Moments later Naruto cracked opened her eyes seeing her vision was blurry again as she glanced around to see where was she.

" Where am I?" She spoke looking at herself in a hospital gown while her vision was starting to adjust.

She paused by looking around her surroundings she was hoping this was a dream she couldn't be in a hospital she slowly got up out the bed but fell trying to stand herself up as she looked around as she turned towards the sun which blinded her as she stepped away and shielded her eyes from the sunlight.

Wait the Sun? she realized something just now she was in the hospital and finds herself in sunlight that only meant one thing.

She was rescued.

" Where a-" before she could speak the hospital doors opened revealing Two Anbu with a weasel mask and neko mask and a Doctor Who looked shocked.

her eyes narrowed when she saw the anbu.

" Naruto you're awake..." Spoke Neko

" Who are you...? how do you know my name?' She spoke with venom.

" Don't you remember us?" asked Weasel

" No... I don't where am I..?" Naruto asked.

" You're in konoha..." The doctor answered.

That was all Naruto needed to know... her face went into shock hearing what the doctor said her eyes narrowed... konoha had rescued her?

" Where is your Hokage...?" She said with disdain in her voice.

" We will inform him immediately... just stay where you are your safe here.. Naruto." Spoke Weasel while Neko nodded did a body flicker to report to the Hokage.

Naruto sat down not looking pleased and not happy with where she is at... for the past two years they finally found her and rescued her.

She wanted to run out of here and escape from konoha but couldn't she wasn't at full strength she needed to eat to get her strength back up all she had to do was wait till they brought the Hokage.

Weasel was watching Naruto like a hawk to him she looked somewhat beautiful and exotic.

The doctor wanted to come by and check Naruto only for her tail to whip out and point at the doctor.

" Don't touch me..." Naruto warned not trusting the doctor as she stepped away in fear a bit of what Naruto could do to her.

 _" She seems to be hostile towards doctors..."_ Thought Weasel.

It wasn't long till Neko and the Hokage finally came while Naruto turned her glance towards him.

" Hello... Hokage-san..." She said with no emotion as he flinched at her tone.

" Naruto..." He whispered... sadly at how cold she was.

 _To be continued._ **AN: OK that's a rap next chapter is coming next week tell me how you liked it? Elf kitsune is coming in three days or two days I hope you enjoyed it those three in Naruto's mindscape with kyuubi was Queen Xenomorph, Sil, ( from species I prefer to use her instead of Eve) and Sarah Kerrigan they will meet Naruto when she graduates from academy and she might reveal her powers. I'm planning on making Naruto dark in this Story or grey.. I'll change the name to Naruko in chapter 3 ok. And for the pairings and junk I'm just gonna make it a flat out harem maybe. and why grey Naruko? or Dark Naruko given how Danzo changed her she is gonna be cold a cold empress she hates humans so yeah her alien nature and instincts will change her but do not worry she won't hate everyone in konoha though and yeah I'm gonna have jiraiya and Tsunade come to the village and see Naruko if you have any questions Pm me or say your suggestions in the review box and I'll read them see you later.**


	3. chapter 3

**An: Here is chapter three not go to say much on the an just going to make this chapter short alright? so enjoy.**

Chapter three: Discussion with the hokage.

Naruto locked her cold black eyes at Hiruzen who looked at her with sadness.

" Naruto... " He spoke softly looking at her features.

" Hokage-san..." She said in a monotone as he winced walking towards her.

They both locked eyes at each other as Hiruzen just stared at his surrogate grandson turned girl.

" Naruto... I am so sorry for not being able to protect you from danzo I have been looking for you two years and I just discovered what kind of treasonous things Danzo has done please forgive me.. I tried sending all of my best anbu and jonins to find you...but there was no trace of you... I almost lost hope that you couldn't be found... but haven't when last night I learned of what Danzo did and that he was the one responsible for kidnapping you" He said in a pleading tone while she stared at him with her black eyes.

She wanted to be angry at him but held her emotional and stayed calm.

" Where is Danzo...?" She whispered but Hiruzen heard her.

" Danzo... has escaped Naruto... when me and my anbu raided his base we were too late to stop him however he is now a traitor and is marked with a bounty so high that missing nins or Hunter nins will go after him where ever he is he will be found and will be brought to Justice for what's he's done to you and all the crimes he's caused I promise you this" Hiruzen said with authority in his tone while Naruto clenched her fists in anger hissing at what she heard Danzo escaped? how was she going to gain her revenge with him now missing.

 _" I will kill you Danzo... once I get stronger this ' weapon' as you call me will kill you..."_ Thought Naruto with anger narrowing her eyes.

Hiruzen noticed how angry she is and could feel hatred rolling off her at the mention of Danzo.

" Naruto..." He said gaining her attention.

" In a day or two you have to stay in the hospital my students are coming to see you.." He said while she gasped.

" I can't stay here Hokage-san..." She said shocking everyone in the room including Hiruzen.

" Why is that Naruto?" He asked winced hearing her call him Hokage-san and not Hokage-jiji.

" Because I can't trust your people here in this village if they tend to get hostile towards me... because if they do... I won't be responsible for what happens to them..." She said in a chilly voice

" Naruto you have to stay... I can't let you go..." He said with her glaring at him.

" And why not? I want to leave this village!" She yelled leaking killer intent surprising the Hokage, Yugao, Itachi and the doctor.

" You expect me to stay in a village that hates me and doesn't want nothing to do with me!?" She yelled leaking more killer intent at them while she was unaware that the walls and ceilings were cracked by her power that she unleashed Hiruzen, Itachi and Yugao widened their eyes at her and this power that she was unleashing was cracking the walls, ceilings and ground.

" _This power what is it!?"_ Thought Itachi with his Sharingan on but cringed and touched his eyes since the power Naruto radiated effected his eyes.

" _My kami what is this!?"_ Thought Yugao who flinched feeling this power while the doctor flinched and backed away.

" _This power what is it.. could it be the kyuubi's? no it's something else"_ Thought Hiruzen trying to find a way to calm naruto down before things get worse.

" Na-Naruto please calm down I know you don't trust the villagers and have every right to be angry at them but it's for your own good you have to stay here konoha is your home!" Hiruzen said trying to reason with her.

" Home? this place isn't home to me!? you expect me to stay here and go through all the abuse your people give me!" She screamed with her power rising cracking windows and destroying everything else around her.

" Please naruto I thought you want to be hokage that's your dream right?" Said Hiruzen while she chuckled darkly.

" Me being hokage? yeah right! why would I want to be hokage when the villagers can't even acknowledge me!" she shouted.

" Naruto please stay here konoha is your home just give it a chance! I promise you once you become a chunin or jonin I will grant you your wish to leave as you please!" Said Hiruzen while Naruto glared at him before calming down.

" You promise to keep your part of the deal?" She asked not sure if she could trust him.

" Yes once you reach jonin I will grant you sannin like status to let you travel" He said nodding while her eyes hardened.

" Fine I will stay here..." She said with a sigh.

" Good naruto I promise I will make this up to you once my students get here to check on you I will enroll you to the shinobi academy" He said with her frowning but nodded

" Good is my apartment still up?" She asked while the Hokage winced.

" I'm afraid not the villagers burned it down..." He said with her eyes narrowed.

" Then I'm living somewhere else... I'm living in the forest..." She said with Hiruzen look at her like she was crazy.

" Naruto are you sure you want to live in _that_ forest?" He asked with her nodding

" Yes the forest of death will be my home.. my forest... I can't stay in the village... besides Danzo once sent me in a forest alone for a week... for survival" She said with coldness in her tone while Hiruzen frowned as did Itachi and Yugao.

" Very well the forest of death will be your home but you're still going to the academy my students will be here soon I'm waiting on their reply.." He said with her staring at him.

" As you wish..." She said sitting back on the hospital bed.

" I expect everything to be requested." She said

" Naruto Neko and Weasel are your personal bodyguards for now on and this doctor will be your personal doctor alright?" He said while she gave them a glance.

" Okay" She said.

" I will see you later Naruto I got business in the office I'll see you when I'm done with paperwork let me know if you need anything" He said motioning Itachi and Yugao to follow him walking out the door leaving naruto alone with her doctor.

" Listen you two are now full time bodyguards for Naruto understood?" He said with them nodding.

" Anko will be joining you two she will be the third bodyguard since Naruto decided to live in the forest of death and no one knows that place better than Anko." He said.

" You three are her bodyguards... we must do everything in our power to keep Naruto here in the village" He said shocking the two.

" Your not holding your part of the deal she mentioned?" Asked Itachi as the Hokage signed.

" No she has to stay here...I can't let her leave as she pleases" He said

" Hokage-sama with all due respect you can't just keep her here forever... If she finds out you didn't keep your part of the deal she will go beserk on this village" Yugao said with him sighing since she was right.

" I'm sorry Yugao but she has to stay in the village... naruto is too important and she's very valuable" He said now thinking about Minato's last wish.

Itachi's eyes widened instantly putting two and two together at what the Hokage was getting at.

" _Naruto is the yondaime's legacy..."_ He thought

" Itachi you stand guard here, Yugao go get Anko and tell her to meet me at my office." He said while Itachi nodded Yugao nodded and shunshiñed to get Anko while the Hokage himself vanished in a swirl of leafs.

 _" Jiraiya... Tsunade I hope the two of you get my message"_ Hiruzen thought

( Mt. Myoboku)

Jiraiya sat on the ground with his legs crossed reading the message he got from his sensei narrowing his eyes at what was said in the letter once he finished he balled it up and tossed it.

" _Sensei how could you let Danzo do this!? I hope he hasn't done to much damage to Naruto's seal!"_ The toad sage thought with anger now getting up from his position to leave to konoha to see what happened to his godson

( Elsewhere at a hotel)

" Tsunade-sama here's a message it's from your sensei" Said a woman with black hair with a pig wearing beads and clothes.

" Tch what does that old monkey want now?" said Tsunade now opening the message reading what was said in the message while her eyes widened then narrowed at what was written in the letter.

" Shizune pack up we're going to konoha" She growled shocking her student

" _Sensei better have a good reason for summoning me back"_ Thought Tsunade who growled.

 _to be continued_

 **AN: I hope you enjoyed it i don't have much to say but I'd like to see your reviews in the next chapter Naruto will have her name changed and will meet Tsunade and Jiraiya until later see you.**


	4. Chapter 4

**An: Hello reader's enjoy the chapter don't have much to say** **and the chapter will be short**

Chapter 4: Arrival of Tsunade and Jiraiya

Two days later in konoha both Jiraiya and Tsunade along side her assistant shizune had returned to see what the sandaime Hokage wanted and why did he send a threat message to Tsunade.

" You better have some excuse for threatening me Sensei!" Yelled Tsunade who looked at her former sensei who was glaring at her

" I will not tolerate your anger Tsunade I have called you and Jiraiya and it concerns your God child!" Hiruzen said with Jiraiya now speaking

" What has happened to Naruto Sensei what the hell did Danzo do!?" Demanded Jiraiya pissed still

" Calm down Jiraiya... and let me explain... Danzo kidnapped Naruto the moment Naruto was kicked out of the orphanage and took him away, I searched for him for two years... that was until I discovered Danzo took Naruto and experimented on him..." Hiruzen explained with Shizune and Tsunade widening their eyes with Jiraiya looking livid

" How could you let this happen!? how could you let Danzo experiment on Minato's child! Minato and Kushina would be rolling over their graves for what you let happen!" Jiraiya yelled with Hiruzen looking away.

" I have tried to protect naruto... jiraiya I have tried my best!" Said Hiruzen.

" Bull shit! if that was true then you would had never let Danzo get away with this!" Scowled Jiraiya

" Danzo will not go unpunished! which is why I ask you to have your spy network to find him!" Spoke Hiruzen

" You damn right I will have my spy network look for that geezer!" Yelled Jiraiya with anger with Tsunade not looking pleased.

" And why did you call me Sensei!" Tsunade exclaimed with him looking at her.

" I called you here for a reason I need you to heal Naruto and check on her..." The sandaime stated with Tsunade frowning

" And why can't the doctors check on her?" She asked

" Because She doesn't trust any doctors and she's been quite Hostile towards them as well..." He said sighing and at the same time cursing Danzo for having his own private doctors to torment Naruto and experiment on her.

" Please Tsunade you and Jiraiya have to take your responsibilities as Naruto's god parents she needs you both I tried everything in my power to protect her from the villagers anger and hatred. i have failed Minato and Kushina.. the villagers refuse to give up on their hate for Naruto" Pleaded the Sandaime

" We will fix this Sensei.. but when I get my hands on him I will be the one to kill him!" Jiraiya said

" No.. Jiraiya... leave Danzo to me after all he was my former team mate it's my responsibility to deal with him" Spoke The sandaime in a hardened tone

" Don't place that on yourself... this is just like what happened to Orochimaru" Spoke Tsunade with Hiruzen frowning then looking down at the mention of his pupil turned traitor.

" Still this has to be done... will you two try speaking to Naruto and check on her" Spoke Hiruzen in a soft tone.

" We will sensei I well check on her seal to make sure Danzo didn't tamper with the seal" Said Jiraiya with a small smile

" Becareful you two... Naruto used to be cheerful and happy plus full of energy... and because of Danzo she became cold.. and doesn't trust anyone not even me..." He said sadly with them flinching as they walked out the door leaving him alone

" _Please try to break the ice in Naruto's heart Jiraiya and Tsunade..."_ Pleaded Hiruzen in thought.

 _To be continued_

 **An: Well there it is hope you enjoyed it next chapter will come soon**


	5. Chapter 5

**An: Okay here goes Kitsune Empress! It's back!**

Chapter 5: The Godparents

( With Naruto)

Sitting on her hospital bed glancing at the window as she began having thoughts about her imprisonment and locked in captivity by Danzo who made her into a Monster... she missed being a Boy... and everything she missed her old life.. but those days were over the moment danzo had experimented on her. She swore when she gets stronger she will seek out for Danzo and kill him... she will have her revenge and no one will deny it from her, not even the Hokage will.

For years she has longed to kill him after what he did to her, Now he has escaped and is no doubt hiding in exile, but don't worry because hiding won't save him from her vengeance and that was a promise...

A Knock at the door alerted her as she turned towards it seeing it open revealing A Blonde haired woman and man with white hair.

"Who are you two?" Naruto Asked glaring at both Tsunade and Jiraiya.

The two flinched who could only look at Naruto in shock and deep regret, As Jiraiya started to talk with some courage in his voice.

"Hi... Naruto... I'm Jiraiya of the Sanin, toad summoner and is a student under the Sandaime Hokage, and this beautiful woman right here is Tsunade Senju" Jiraiya introduced making the Senju woman form a smile

Naruto eyed the two before her as she recalled visiting The Sandaime's office and saw a picture of the old Kage and his students frowning feeling not interested in the two she spoke

"What do you two want?" She Said rather coldly making both adults wince

 _"Such coldness..."_ Thought Tsunade sadly for her God Daughter

 _"Damn you Danzo... Damn you to Hell for making her like this!"_ Jiraiya mentally Yelled in Thought really wanting to go and kill Danzo.

"Naruto... we want to help you... please?" Jiraiya Asked Seeing her look at him with less interest

"I don't need any help... " she said closing her eyes.

"Please Naruto, I'm a healer allow me to bring you back to strength... and let Jiraiya check on your seal" Said Tsunade looking at the hybrid girl

"A healer you say? I guess it won't hurt.. what I really need is food... but I'd liked to be healed" Naruto Said calmly

"May I check on your seal Naruto?" Asked Jiraiya Who saw the girl frown and nod slightly.

Tsunade began using her diagnostic Jutsu scanning and looking at Naruto and could see that Naruto isn't hardly human anymore whatever Danzo experimented her with turned her into a creature of some sort so far she's found three types of Dna's she couldn't describe within Naruto's molecules and genes and wondered what made her change a different sex. What amazed her was that Naruto's blood was no longer red, it was highly green and yet acidic.

Jiraiya was looking over Naruto's Kyuubi seal and could see that Danzo didn't damage it or ruin it in anyway. But his eyes widened then narrowed when he saw another Seal on the back of Naruto's neck and it just wasn't any seal! It was a loyalty Seal! That bastard placed the seal on her just Incase she steps out of line she has to obey him like his mindless root! He immediately rid of the seal before Danzo could activate it he couldn't risk Naruto being turned into Danzo's puppet.

"Are we done or what?" She asked rather impatient

"Well you're healthy so far and you look like your in good condition" Said Tsunade as Naruto turned towards Jiraiya

"Your Seal seems fine, lucky that Danzo didn't tamper with it" He Said looking at her then at Tsunade.

"Well I appreciate you two for checking on me... do return to your sensei.." Naruto Said blankly

"But Naruto we want to stay here and talk to you..." Tsunade Said with worry

"There's nothing to talk about" She Said sarcastically

"Yes there is... Naruto we are your god parents" Jiraiya Said as Naruto paused as the temperature in the room began to drop absolute zero as the walls and ceilings started cracking, the windows Shattered! as her whole room started to tremor.

"What did you SAY!?" She hissed!

 _To be continued_

 **An: Well there it is! Had to come up with something for this chapter until next time**


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